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Reproducible Research Practices and Transparency across the Biomedical Literature
Reproducible Research Practices and Transparency across the Biomedical Literature
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Reproducible Research Practices and Transparency across the Biomedical Literature

PLoS biology, 2016-01, Vol.14 (1), p.e1002333-e1002333 [Peer Reviewed Journal]

2016 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Iqbal SA, Wallach JD, Khoury MJ, Schully SD, Ioannidis JPA (2016) Reproducible Research Practices and Transparency across the Biomedical Literature. PLoS Biol 14(1): e1002333. doi:10.1371/journal.pbio.1002333 ;ISSN: 1545-7885 ;ISSN: 1544-9173 ;EISSN: 1545-7885 ;DOI: 10.1371/journal.pbio.1002333 ;PMID: 26726926

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2
Cancer research needs a better map
Cancer research needs a better map
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Cancer research needs a better map

Nature (London), 2021-01, Vol.589 (7843), p.514-516 [Peer Reviewed Journal]

COPYRIGHT 2021 Nature Publishing Group ;Copyright Nature Publishing Group Jan 28, 2021 ;ISSN: 0028-0836 ;EISSN: 1476-4687 ;DOI: 10.1038/d41586-021-00182-0 ;PMID: 33500573

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3
Adherence to Methodological Standards in Research Using the National Inpatient Sample
Adherence to Methodological Standards in Research Using the National Inpatient Sample
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Adherence to Methodological Standards in Research Using the National Inpatient Sample

JAMA : the journal of the American Medical Association, 2017-11, Vol.318 (20), p.2011 [Peer Reviewed Journal]

EISSN: 1538-3598 ;DOI: 10.1001/jama.2017.17653 ;PMID: 29183077

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4
Making data sharing the norm in medical research
Making data sharing the norm in medical research
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Making data sharing the norm in medical research

BMJ, 2023-07, Vol.382, p.1434-1434 [Peer Reviewed Journal]

Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go tohttp://group.bmj.com/group/rights-licensing/permissions2023BMJ ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 1756-1833 ;ISSN: 0959-8138 ;EISSN: 1756-1833 ;EISSN: 1468-5833 ;DOI: 10.1136/bmj.p1434 ;PMID: 37433610

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5
Ethical challenges of big data in public health
Ethical challenges of big data in public health
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Ethical challenges of big data in public health

PLoS computational biology, 2015-02, Vol.11 (2), p.e1003904-e1003904 [Peer Reviewed Journal]

COPYRIGHT 2015 Public Library of Science ;COPYRIGHT 2015 Public Library of Science ;2015 Vayena et al 2015 Vayena et al ;2015 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Vayena E, Salathé M, Madoff LC, Brownstein JS (2015) Ethical Challenges of Big Data in Public Health. PLoS Comput Biol 11(2): e1003904. doi:10.1371/journal.pcbi.1003904 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003904 ;PMID: 25664461

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6
Use of the p-values as a size-dependent function to address practical differences when analyzing large datasets
Use of the p-values as a size-dependent function to address practical differences when analyzing large datasets
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Use of the p-values as a size-dependent function to address practical differences when analyzing large datasets

Scientific reports, 2021-10, Vol.11 (1), p.20942-20942, Article 20942 [Peer Reviewed Journal]

2021. The Author(s). ;The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2021 ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/s41598-021-00199-5 ;PMID: 34686696

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7
Validation in prediction research: the waste by data splitting
Validation in prediction research: the waste by data splitting
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Validation in prediction research: the waste by data splitting

Journal of clinical epidemiology, 2018-11, Vol.103, p.131-133 [Peer Reviewed Journal]

2018 Elsevier Inc. ;Copyright © 2018 Elsevier Inc. All rights reserved. ;Copyright Elsevier Limited Nov 2018 ;ISSN: 0895-4356 ;EISSN: 1878-5921 ;DOI: 10.1016/j.jclinepi.2018.07.010 ;PMID: 30063954

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8
The AIMe registry for artificial intelligence in biomedical research
The AIMe registry for artificial intelligence in biomedical research
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The AIMe registry for artificial intelligence in biomedical research

Nature methods, 2021-10, Vol.18 (10), p.1128-1131 [Peer Reviewed Journal]

COPYRIGHT 2021 Nature Publishing Group ;Springer Nature America, Inc. 2021. ;ISSN: 1548-7091 ;ISSN: 1548-7105 ;EISSN: 1548-7105 ;DOI: 10.1038/s41592-021-01241-0 ;PMID: 34433960

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9
Recommendations for the responsible use and communication of race and ethnicity in neuroimaging research
Recommendations for the responsible use and communication of race and ethnicity in neuroimaging research
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Recommendations for the responsible use and communication of race and ethnicity in neuroimaging research

Nature neuroscience, 2024-04, Vol.27 (4), p.615-628 [Peer Reviewed Journal]

2024. Springer Nature America, Inc. ;Springer Nature America, Inc. 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. ;ISSN: 1097-6256 ;EISSN: 1546-1726 ;DOI: 10.1038/s41593-024-01608-4 ;PMID: 38519749

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10
Dimensionality reduction for visualizing single-cell data using UMAP
Dimensionality reduction for visualizing single-cell data using UMAP
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Dimensionality reduction for visualizing single-cell data using UMAP

Nature biotechnology, 2019-01, Vol.37 (1), p.38-44 [Peer Reviewed Journal]

COPYRIGHT 2019 Nature Publishing Group ;COPYRIGHT 2019 Nature Publishing Group ;Copyright Nature Publishing Group Jan 2019 ;ISSN: 1087-0156 ;EISSN: 1546-1696 ;DOI: 10.1038/nbt.4314 ;PMID: 30531897

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11
Timing of high-efficacy therapy for multiple sclerosis: a retrospective observational cohort study
Timing of high-efficacy therapy for multiple sclerosis: a retrospective observational cohort study
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Timing of high-efficacy therapy for multiple sclerosis: a retrospective observational cohort study

Lancet neurology, 2020-04, Vol.19 (4), p.307-316 [Peer Reviewed Journal]

2020 Elsevier Ltd ;Copyright © 2020 Elsevier Ltd. All rights reserved. ;2020. Elsevier Ltd ;ISSN: 1474-4422 ;ISSN: 1474-4465 ;EISSN: 1474-4465 ;DOI: 10.1016/S1474-4422(20)30067-3 ;PMID: 32199096

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12
Implementing clinical trial data sharing requires training a new generation of biomedical researchers
Implementing clinical trial data sharing requires training a new generation of biomedical researchers
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Implementing clinical trial data sharing requires training a new generation of biomedical researchers

Nature Medicine, 2023-02, Vol.29 (2), p.298-301 [Peer Reviewed Journal]

Springer Nature America, Inc. 2023. ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 1078-8956 ;EISSN: 1546-170X ;EISSN: 1744-7933 ;DOI: 10.1038/s41591-022-02080-y ;PMID: 36732626

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13
Gender imbalance in medical imaging datasets produces biased classifiers for computer-aided diagnosis
Gender imbalance in medical imaging datasets produces biased classifiers for computer-aided diagnosis
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Gender imbalance in medical imaging datasets produces biased classifiers for computer-aided diagnosis

Proceedings of the National Academy of Sciences - PNAS, 2020-06, Vol.117 (23), p.12592-12594 [Peer Reviewed Journal]

Copyright © 2020 the Author(s). Published by PNAS. ;Copyright National Academy of Sciences Jun 9, 2020 ;Copyright © 2020 the Author(s). Published by PNAS. 2020 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.1919012117 ;PMID: 32457147

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14
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy
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HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

Journal for immunotherapy of cancer, 2021-04, Vol.9 (4), p.e002071 [Peer Reviewed Journal]

Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY. Published by BMJ. ;2021 Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY. Published by BMJ. This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See https://creativecommons.org/licenses/by/4.0/ . Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY. Published by BMJ. 2021 ;ISSN: 2051-1426 ;EISSN: 2051-1426 ;DOI: 10.1136/jitc-2020-002071 ;PMID: 33858848

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15
Artificial intelligence foundation for therapeutic science
Artificial intelligence foundation for therapeutic science
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Artificial intelligence foundation for therapeutic science

Nature chemical biology, 2022-10, Vol.18 (10), p.1033-1036 [Peer Reviewed Journal]

Springer Nature America, Inc. 2022. ;ISSN: 1552-4450 ;EISSN: 1552-4469 ;DOI: 10.1038/s41589-022-01131-2 ;PMID: 36131149

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16
Estimating the success of re-identifications in incomplete datasets using generative models
Estimating the success of re-identifications in incomplete datasets using generative models
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Estimating the success of re-identifications in incomplete datasets using generative models

Nature communications, 2019-07, Vol.10 (1), p.3069-9, Article 3069 [Peer Reviewed Journal]

2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2019 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-019-10933-3 ;PMID: 31337762

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17
Toward a Shared Vision for Cancer Genomic Data
Toward a Shared Vision for Cancer Genomic Data
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Toward a Shared Vision for Cancer Genomic Data

The New England journal of medicine, 2016-09, Vol.375 (12), p.1109-1112 [Peer Reviewed Journal]

Copyright © 2016 Massachusetts Medical Society. All rights reserved. ;ISSN: 0028-4793 ;EISSN: 1533-4406 ;DOI: 10.1056/NEJMp1607591 ;PMID: 27653561

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18
A comparison of automatic cell identification methods for single-cell RNA sequencing data
A comparison of automatic cell identification methods for single-cell RNA sequencing data
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A comparison of automatic cell identification methods for single-cell RNA sequencing data

Genome Biology, 2019-09, Vol.20 (1), p.194-194, Article 194 [Peer Reviewed Journal]

2019. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s). 2019 ;ISSN: 1474-760X ;ISSN: 1474-7596 ;EISSN: 1474-760X ;DOI: 10.1186/s13059-019-1795-z ;PMID: 31500660

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19
Revolutionizing cardiovascular medicine: targeted therapies for the cardiac conduction system
Revolutionizing cardiovascular medicine: targeted therapies for the cardiac conduction system
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Revolutionizing cardiovascular medicine: targeted therapies for the cardiac conduction system

The Journal of clinical investigation, 2022-10, Vol.132 (20), p.1-3 [Peer Reviewed Journal]

Copyright American Society for Clinical Investigation Oct 2022 ;ISSN: 0021-9738 ;EISSN: 1558-8238 ;DOI: 10.1172/JCI156955

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20
Visualizing a field of research: A methodology of systematic scientometric reviews
Visualizing a field of research: A methodology of systematic scientometric reviews
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Visualizing a field of research: A methodology of systematic scientometric reviews

PloS one, 2019-10, Vol.14 (10), p.e0223994-e0223994 [Peer Reviewed Journal]

COPYRIGHT 2019 Public Library of Science ;COPYRIGHT 2019 Public Library of Science ;2019 Chen, Song. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2019 Chen, Song 2019 Chen, Song ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0223994 ;PMID: 31671124

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